Sequence
atgc intronic sequence ATGC exonic sequence...tttttttttatgaatgattagttaacacgtgaaatcttcgatgtagaacaacctttttatgacttataaattaatgatgttgtgcattaaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA
Basic information
species | Glycine max |
transcript | GLYMA03G32130.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 7
---tttttttttatgaatgattagttaacacgtgaaatcttcgatgtagaacaacctttttatgacttataaattaatgatgttgtgcattaaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA
| | || | || || | || | || | || | || | | | | | ||| || | | | || || ||||||||||||||| |||||||| |||||||| || ||||| |||||||||||||| || || ||||| || |||| || ||||| |||| ||| |
ttactactgattgtttgtgtttggatagt-tatcaacttgtcatgattatactaaggatatgtcctctgtaattttactcaaatctaatttgtatat--gcagGTGTGAAGCATTCTCAACCTATCCTCGAACATATGATCTTCTCCATGCATGGACAGTCTTCTCTGACCTTGACAAGAGAGGTTGCAGCGCAGAAGATCTC
upper sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 7
tttttttttatgaatgat-tagttaacacgtgaaatcttcgatgtag-aacaacctttttatg-acttataaattaatgatgttgtgcattaaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA
||| | | || || | || || || | | || | | |||| | | || | |||||| | | | | | | | | || |||||||||||| || |||||||| |||||||| |||||||| ||||| |||||| | || |||||||| || ||| | || |||||| | || || |
tttgcaatcaagattgtcattattggcaggttt--ccgtagaagcgggaacatcgtgcttccacatttataattcactcaaatccaataatgcgttttg-cagGTGTGAAGCCTTCTCAACCTATCCTCGAACATACGATCTTCTCCACGCATGGGCAGTCTTTTCTGACCTTGATAAAAGAGGCTGCAGTGCCGAAGACCTG
upper sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 6
tttttttttatgaatgattagttaacacgtgaaatcttcgatgtagaacaacctttttatgacttataaattaatgatg-----ttgtgcat-taaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA
|||| || | | | | | | | | ||| ||||| || || ||| | ||| | | ||||| || |||||||||||||||| || ||||||||||| ||||| ||||| ||||||||||| ||||| || || |||||||| || | || ||| |||||||||||
-----cattataaaaggcacgaccatttcttttagagttg-taaagattgttcttttccagatcaatgaatcactgaaggatcttcttgcatgccaactctgacagGTGTGAAGCCTTCTCAACCTACCCACGAACCTACGACCTACTCCATGCCTGGACCGTCTTCTCTGATATAGAGCGAAATGGGTGTAGTGCAGAGGATTTA
upper sequence: GLYMA03G32130.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S140_59V6.2 (Physcomitrella patens), 3'ss of exon 7
--------tttttttttatgaatgattagttaacacgtgaaatcttcgatgtagaacaacctttttatgacttataaattaatgatgttgtgcattaaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA
| ||| | | || || | || | | || | ||| |||| | ||| | | || |||| ||| |||| | |||||||||||| ||||| || ||||| || || |||||||| || |||||||||||||| || || |||||| | ||| | ||||| | ||| |
catttacaatatttgtcgtacttgtttgtgtcgcaattttggctaggattttataggaacgttttga--gcttgaacttgaagtatgtggtg----gaatgtt--cagGTGTGAAGCTTTTTCGACATACCCGCGCACATACGATCTGCTGCATGCATGGACTGTATTCTCAGATATTGAGGATAAAAACTGCAGAATTAAAGATCTTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|12774574|gb|BG239501.1|BG239501EST: NNTCTCAAGATAATATACGACAGAGGACTGATAGGAACAGTTCACAACTG GTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATG
genomic: AATCTCAAGATAATATACGACAGAGGACTGATAGGAACAGTTCACAACTGgtatggctcg ... atgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATG
EST:
gi|8825745|gb|BE209411.1|BE209411EST: NNTCTCAAGATAATATACGACAGAGGACTGATAGGAACAGTTCACAACTG GTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATG
genomic: AATCTCAAGATAATATACGACAGAGGACTGATAGGAACAGTTCACAACTGgtatggctcg ... atgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacaacctttttatgacttataaattaatgatgttgtgcattaaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA
aattaat putative branch site (score: 3)
tttttatgacttataa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttttatgaatgattagttaacacgtgaaatcttcgatgtagaacaacctttttatgacttataaattaatgatgttgtgcattaaatgctgacagGTGTGAAGCATTTTCAACCTACCCTCGAACGTACGATCTACTCCATGCATGGACTGTGTTTTCTGATATTATTAAGAAAGAATGCAGTCCAGAGGATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT